package core.aln;

/*Author: John Archer, Contact: john.archer.jpa@gmail.com*/
public class Aligner {
    public int go, ge;
    public int mis, mat;
    public char gap;

    public Aligner(int gp, int ge, int mat, int mis) {
        this.go = gp;
        this.ge = ge;
        this.mat = mat;
        this.mis = mis;
        this.gap = '-';
    }

    protected double maxVal(double[] vals) {
        double mVal = vals[0];
        for (int z=0; z<vals.length; z++){if(vals[z]>mVal){mVal=vals[z];}}
        return mVal;
    }
    
    protected double pPara(char c1, char c2) {
        if (c1==c2) {return mat;}
        return mis;
    }
}